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[R-pkgs] New Quantian release with over 800 CRAN/BioC packages

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[R-pkgs] New Quantian release with over 800 CRAN/BioC packages

Dirk Eddelbuettel

[ Reposting this here as this Quantian release contains
   - all CRAN packages as of December 10, 2005
      * except the Windows only ones (BRugs, mimR, rcom, RWinEdt)
      * and three that would not build (Rlsf, ROracle, rJava) for lack of
        Java, Oracle or rlsf
   - all BioC packages for release 1.8
      * excecpt RMAGEML (needs Java)
   - for a total of over 800 R packages
   - a couple other R niceties: (X)Emacs + ESS, Ggobi, Rpad, RKward...)
  I hope this isn't considered off-topic here; if so please let me know
  in private mail and I will refrain from posting in the future.  -- Dirk ]



(Please see note [1] below regarding recipients for this posting. Thanks!)


Executive Summary:

    Quantian 0.7.9.1 is the first Quantian release based on Knoppix 4.0.2.
    Quantian adds hundreds of scientific / numeric packages, as well as the
    openMosix enabled 2.4.27 kernel, to the cdrom version of Knoppix.
   
    Relative to the previous release 0.6.9.3, hundreds of applications have
    been updated, and many new applications (such as polyxmass, scigraphica,
    kst, octaviz, gromacs) have been added. Quantian now contains over 2400
    Debian packages, and over 800 packages for R.

    Quantian comes as one bootable dvd iso of 2.5gb (compressed) with
    almost 7 gb (uncompressed) of software of interest to quantitative
    analysts, scientists, researchers or students.


Announcing Quantian release 0.7.9.1
===================================


I   What is it?

    Quantian is a remastering of Knoppix, the self-configuring and directly
    bootable cdrom/dvd that turns any pc or laptop into a full-featured Linux
    workstation, and (parts of) clusterKnoppix, which adds support for
    openMosix-based  cluster computing. However, Quantian differs from
    Knoppix by having a particular focus on quantitative, numerical or
    scientific applications, and hence adds a very large set of programs of
    interest to applied or theoretical workers in quantitative or data-driven
    fields to the solid base provided by Knoppix.

    See http://dirk.eddelbuettel.com/quantian.html for more details.

   
II What Quantian highlights should I care about ?

    o First release based on Knoppix 4.0.2: Derived from the cdrom version of
      Knoppix, Quantian utilises the unionfs setup of Knoppix to combine two
      compressed loop images for a total of 2.5 gb (from two files of 2.0 gb
      and 425 mb) corresponding to almost 7 gb of software.

    o KDE 3.4, Kernel 2.6.12; added backport of kernel 2.4.27 with openMosix
      patch for continued openMosix support [ but note that openMosix and
      unionfs seem to conflict so kernel 2.4.27 only sees the first
      compressed loop image ]

    o Some highlights in 0.7.9.1 are
     
      - very complete R support with over 800 packages (28 from 'core R',
        another 70 from Debian packages, and 724 directly installed from
        CRAN and BioConductor, covering over 99% of all packages at CRAN
        and BioConductor [ not counting a handful of windows-only CRAN
        packages ] ), ESS editing in Emacs/XEmacs, GGobi visualization,
        Rpad webinterface, and initial support for the RKward GUI;

      - even stronger bioinformatics/biology support than before:
        BioConductor, arb, biofox, bioperl, biopython, blast2, boxshade,
        bugsx, clustalw, fastdnaml, fastlink, garlic, gromacs, hmmer, loki,
        mipe, molphy, muscle, ncbi, phylip, rasmol, readseq, seaview,
        t-coffee, textopo, and more;

      - continued strong mathematics / computational algrebra support: axiom,
        blacs, calc, euler, gap, giac, mathomatic, maxima, pari, scalapack,
        scilab, texmacs, yacas, yorick;

      - strong visualization / graphics support: dx, garlic, gdpc, gnuplot,
        grace, grass, gri, illuminator, kst, labplot, mayavi, matplot, proj,
        plplot, plotmtv, rasmol, starplot, vtk, xd3d, xgraph, ygraph;
 
      - large number of programming and scripting languages, editors,
        debuggers and libraries;

      - excellent latex support with auctex, lyx, kile, texmacs interface,
        as well as numerous macro packages, bibtex tools;

      - office support via openoffice and koffice suites, abiword, gnumeric
        and other applications;

      - plus all the tools and toys from the current Knoppix relase.

    o See http://dirk.eddelbuettel.com/quantian/changelog.html for details.

    o See http://dirk.eddelbuettel.com/quantian/howto.html for several
      short HOWTOs on booting Quantian from hd on either Windows or Linux,
      booting via a bootcd (such as clusterKnoppix), or botting from a
      USB memory device.  Contributions, corrections, and feedback on these
      HOWTOs is always appreciated.


III Where do I get it?

    o Downloads are available from the main host at Seattle at FHCRC:

            http://quantian.fhcrc.org/
            rsync://quantian.fhcrc.org/quantian/
     
      and at the East Coast at

            http://research.warnes.net/downloads/quantian/CURRENT/
            ftp://research.warnes.net/users/edd/quantian/CURRENT/

      The most recent release is also available at

            http://quantian.alioth.debian.org/

      Note that file size of 2.5 gb may upset web caching system such
      as squid. It may be best to rely on rsync or bittorrent instead
      of http.

    o Bittorrents should be available shortly at

            http://www.tlm-project.org/public/distributions/quantian/

    o The main European mirrors should catch up shortly:

            http://sunsite.rediris.es/mirror/quantian

            http://sunsite.informatik.rwth-aachen.de/ftp/pub/Linux/quantian

    o CD/DVD vendors will probably update their offerings soon as well.
      See the Quantian site for a list.


IV  Mailing lists

    o Two mailing lists exist for Quantian

        quantian-announce  for announcements, intended to be low volume
        quantian-general  for general discussions about Quantian

      available via

        http://alioth.debian.org/mail/?group_id=30303

      for subscription info etc., and start using the quantian-general lists
      for general questions, comments, suggestions or discussions about
      Quantian.

      Quantian-general is subscribed to quantian-announce, so you only need
      to subscribe to one (but can of course subscribe to both).  Posting to
      quantian-general requires a subscription.

      Reply-To: for this message is [hidden email]
      so that discussions can be continued on the list.


V  Known Bugs in 0.7.9.1

    o Debian's current C++ transition affects the KDE packages. Several
      packages had to be installed from the stable relase, and a few
      (celestia, gdal) are currently uninstallable. This should should
      improve over the next few weeks/months.
     
    o Kdvi is broken. However, xdvi works as do the various pdf previewers
      so (PDF)LaTeX use is still possible.

    o As noticed above, when openMosix and kernel 2.4.27 are used, the
      second compressed loop image is not accessible implying that the
      /opt, /usr/games, /usr/lib/j2se, /usr/share/doc, /usr/src, /usr/NX
      directories are not accessible.


VI   Other items

    o Feedback / poll on package additions or removal

      As always, I welcome comments and suggestions about programs to be
      added or removed. Existing Debian packages, and possibly existing
      rpm packages, typically get inserted quite readily.

      Please send feedback, questions, comments, ... to the
     
        [hidden email]

      list to maximise the number of eyes glancing at any one question.
      Notice that a subscription to the list is needed in order to post.

    o Feedback would also be appreciated on ways to better communicate with
      difference scientific communities that could be interested in Quantian.


VII Notes

    [1] This email is sent via the quantian-announce mailing list. I have
        subscribed those whose email addresses are in my quantian mail folder
        due to prior emails. The quantian-announce mailing list only sends
        moderator-approved posts -- so there should be no spam whatsoever.
        Anybody who considers this unwanted is kindly asked to send me a
        private mail to get unsubscribed immediately. Otherwise, replies and
        follow-ups should go to  
                [hidden email]
        where posting may require an initial subscription.



Best regards,  Dirk



--
Hell, there are no rules here - we're trying to accomplish something.
                                                  -- Thomas A. Edison

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